matplotlib-users Mailing List for matplotlib

Hi there.  I'm investigating using matplotlib for plotting of Adaptive
Mesh Refinement (
http://en.wikipedia.org/wiki/Adaptive_mesh_refinement )  data -- the
primary characteristic of which is that it is of non-equal resolution.
 I've used the scipy/delaunay method, as mentioned in the cookbook,
but unfortunately that provides a level of interpolation that is not
always desirable; very often when plotting data, we want to be able to
see clear cell boundaries, as well as boundaries between resolution
levels.

Essentially what I have are the following pieces of data: x, y, dx,
dy, z.  The simplest way is for me to sample this using a loop over
points in the module where I handle the data; however, what I'd like
to be able to do is hand it off to matplotlib, and the on-the-fly
change the x,y (and z) bounds.  (This seems as though it would be the
more efficient manner of handling the data, anyway.)

Is there a way to do this?  If not, would it be terribly difficult for
me to implement?  I've browsed the code, and it seems that the best
starting place would by pcolor in lib/matplotlib/pylab.py or
src/_image.cpp.  I very much would like to leverage the abilities of
matplotlib -- specifically, I'm very excited about being able to plot
this data, and then overplot contour or quiver plots (which I have
done with my data using the delaunay method.)

Any ideas?  Thanks!

-Matt

On 5/31/07, Andrea Gavana <and...@gm...> wrote:
> Hi All,
>
>     I am writing an application (wxPython based) which embeds a big
> matplotlib figure as a main panel. Basically, this app shows oil well
> producers and gas injectors on a 2D map as dots (every dot represents
> its surface location), and a bunch of "streamlines" (i.e., straight
> lines or simple curves) which connect injectors and producers.
> As the numerical simulation continues, more and more streamlines are
> added to the plot (because of new wells or because interference
> between wells), and actually I end up having 200 dots plus 800-1200
> lines. As the simulation progresses, the plots become slower and
> slower...
> As the lines are usually 2-points straight lines, I was thinking about
> using Line Collections; however, every matplotlib line has a linewidth
> value that is dependent on the calculated "interference" effect
> between wells, which means I have to build a matplotlib line for every
> line connecting an injector with a producer. Moreover, every injector
> well has its own colour for the streamlines (there are 33 injector
> wells).
> Will Line Collections save some time in this case? If not, does anyone
> have a suggestion on how I could try to speed-up the plotting? I am
> not really familiar with some obscure line/axes properties, so I may
> have overlooked something.

Yes, a line collection will save you a lot of time with upwards of
1000 line segments.  This is the use case they were designed to solve:
a bunch of segments of differing widths and colors.  One could
optimize it for the special case of simple line segments, ie [(x1,y1),
(x2, y2)] in which case we could use numpy arrays, but currently we
have only the general case of a collection of arbitrary length
segments, and since they are not necessarily the same length, we use a
sequence of segments rather than an array, and this is slower than it
could be.

JDH

Hi All,

    I am writing an application (wxPython based) which embeds a big
matplotlib figure as a main panel. Basically, this app shows oil well
producers and gas injectors on a 2D map as dots (every dot represents
its surface location), and a bunch of "streamlines" (i.e., straight
lines or simple curves) which connect injectors and producers.
As the numerical simulation continues, more and more streamlines are
added to the plot (because of new wells or because interference
between wells), and actually I end up having 200 dots plus 800-1200
lines. As the simulation progresses, the plots become slower and
slower...
As the lines are usually 2-points straight lines, I was thinking about
using Line Collections; however, every matplotlib line has a linewidth
value that is dependent on the calculated "interference" effect
between wells, which means I have to build a matplotlib line for every
line connecting an injector with a producer. Moreover, every injector
well has its own colour for the streamlines (there are 33 injector
wells).
Will Line Collections save some time in this case? If not, does anyone
have a suggestion on how I could try to speed-up the plotting? I am
not really familiar with some obscure line/axes properties, so I may
have overlooked something.
This is with matplotlib 0.90, numpy 1.0.3, wxPython 2.8.4, Python 2.5,
Windows XP, WxAgg (pure Python implementation).

Thank you for every suggestion, and sorry for the long post.

Andrea.

"Imagination Is The Only Weapon In The War Against Reality."
http://xoomer.virgilio.it/infinity77/

Matthew Auger wrote:
> I've recently needed to use matplotlib remotely from a 'server' running OS 
> X. The server does not have GTK on it, and the server's version of Tk is 
> bound to Aqua instead of X11 and I therefore can't remotely spawn a 
> matplotlib GUI window.
>
> My question: Does anyone know of an *easy* way to get a backend running 
> that will allow me to push windows through ssh X11 forwarding? I don't 
> have administrative access on the server, so I'm trying to find the 
> simplest solution possible for the administrator to implement--presumably 
> this rules out GTK....
>
> Thanks!
> Matt
>
> -

Matt: Depends on your definition of 'easy' ...

The fink matplotlib package uses GTKAgg as the default backend, and 
works fine over an ssh tunnel.  The admin will have to:

0) make sure X11.app (and the X11 SDK) is installed.
1) install fink
2) run 'fink selfupdate'
3) run 'fink install matplotlib-py25' (and wait a few hours for 
everything to compile).

HTH,

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

I've recently needed to use matplotlib remotely from a 'server' running OS 
X. The server does not have GTK on it, and the server's version of Tk is 
bound to Aqua instead of X11 and I therefore can't remotely spawn a 
matplotlib GUI window.

My question: Does anyone know of an *easy* way to get a backend running 
that will allow me to push windows through ssh X11 forwarding? I don't 
have administrative access on the server, so I'm trying to find the 
simplest solution possible for the administrator to implement--presumably 
this rules out GTK....

Thanks!
Matt

Hello,

I am trying to use py2app, and it is choking on pytz which is used by matplotlib. 
Reading the py2app docs, and a lot of posts, it seems that the problem I'm having 
isn't common.  Essentially, it is saying that there is no pytz.zoneinfo module.  So I 
checked, with the latest pytz installed, and there is no pytz.zoneinfo module!  There 
is a directory under pytz called zoneinfo, but there is no __init__.py.  Is there 
something I am missing?  Have others managed to get py2app work with an app that uses 
matplotlib?


		thanks,

			Brian Blais

-- 
-----------------

              bb...@br...
              http://web.bryant.edu/~bblais

Take a look at the semilogx and semilogy functions:

=20

http://matplotlib.sourceforge.net/matplotlib.pylab.html#-semilogx

=20

trevis

=20

-----Original Message-----
From: mat...@li...
[mailto:mat...@li...] On Behalf Of
Navid Parvini
Sent: Thursday, May 31, 2007 6:40 AM
To: mat...@li...
Subject: [Matplotlib-users] log scale

=20

Dear All,

How can I set the x-axis and/or y-axis in Log scale.

Thanks,
Navid

 =20

  _____ =20

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On 5/30/07, Jeff Peery <jef...@ya...> wrote:
> Hello, I'm getting this error when using two consecutive plot_dates():
>
>   File "C:\Python24\lib\site-packages\matplotlib\axes.py",
> line 1565, in xaxis_d ate
>     formatter = AutoDateFormatter(locator)
> UnboundLocalError: local variable 'locator' referenced before assignment
>
> I've tested using just three lines of code:
>
> From pylab import *
> plot_date([783746, 783747, 783748], [1,2,3])
> plot_date([783749, 783750, 783751], [1,2,3])

Yes, this is a known bug that is fixed in the svn version of
matplolib.  Thanks for the report.

JDH

On 5/31/07, Navid Parvini <par...@ya...> wrote:
> Dear All,
>
>  I have a code that creates plots using pylab module, using pylab.plot().
>  I want to use the output of this moudule in qt (QImage or QPixmap).


You probably want to embed your matplotlib code directly into qt:

http://matplotlib.sourceforge.net/examples/embedding_in_qt.py
http://matplotlib.sourceforge.net/examples/embedding_in_qt4.py

This means not using the pylab interface but it is a minor translation.  See

http://matplotlib.sourceforge.net/examples/pythonic_matplotlib.py

and

http://matplotlib.sourceforge.net/faq.html#OO

JDH

Hi,

2007/5/31, Navid Parvini <par...@ya...>:
> Dear All,
>
> How can I set the x-axis and/or y-axis in Log scale.

In interactive mode:

plot([1, 1e1, 1e2], [1, 1e1, 1e2])
ax = gca()
ax.set_xscale('log')
ax.set_yscale('log')
draw()

The other parameter .set_xscale and set_yscale accept is 'linear' for,
surprisingly enough, linear scale.


Regards,

    ~ Antonio

Dear All,

How can I set the x-axis and/or y-axis in Log scale.

Thanks,
Navid
 
 
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There are RPMs for SUSE here:
http://software.opensuse.org/download/science/openSUSE_10.2/

though last time I tried to use them they just didn't work (maybe they
do now?). However, having MPL running on SUSE is actually pretty easy.
This is what I've done:

1. From the link mentioned above, install python-numpy and python-scipy
RPMs (and their dependencies).

2. Check on MPL's web-site for the list of RPMs you need before
compiling MPL from source. The list is a not short, but you will find
all the needed RPMs on SUSE's repositories.

3. Download MPL. E.g. to download latest svn version:
svn co https://svn.sourceforge.net/svnroot/matplotlib/trunk matplotlib

4. cd to the downloaded directory, then cd to folder matplotlib in it.

5. As super-user, type:
# python setup.py install

And that's all. That should do.

Antonio


John Pye wrote:
> Hi all
> 
> Can anyone tell me whether or not it is straightforward to run
> matplotlib on OpenSUSE 10.2?
> 
> My project has a dependency on matplotlib and I have a user on that
> platform who tells me that it's not available as an RPM in the SUSE
> repository. Can that really be true?
> 
> Cheers
> JP
> 
> 

Dear All,
 
 I have a code that creates plots using pylab module, using pylab.plot().
 I want to use the output of this moudule in qt (QImage or QPixmap).
 
 Would you please guide me in this regard?
 
 Thank you in advance.
 Navid
  
 
---------------------------------
Bored stiff? Loosen up...
Download and play hundreds of games for free on Yahoo! Games.

Hi all

Can anyone tell me whether or not it is straightforward to run
matplotlib on OpenSUSE 10.2?

My project has a dependency on matplotlib and I have a user on that
platform who tells me that it's not available as an RPM in the SUSE
repository. Can that really be true?

Cheers
JP


-- 
John Pye
Department of Mechanical and Manufacturing Engineering
University of New South Wales, Sydney, Australia.
john.pye AT student DOT unsw.edu.au

Hi Alan,

I'm not speaking for anyone else, but as far as I'm concerned that code is 
public domain.

Cheers,
Brett.




Alan G Isaac <ai...@am...> 
Sent by: mat...@li...
31/05/2007 01:17 PM
Please respond to
ai...@am...


To
Matplotlib Users <mat...@li...>
cc

Subject
Re: [Matplotlib-users] Handling  LARGE data sets






On Thu, 31 May 2007, bre...@un... apparently wrote: 
> Here is a decimating filter module based on the 
> Savtsky-Golay method. 

License?
Is there a presumption that code posted to this
list is public domain?

Cheers,
Alan Isaac



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On Thu, 31 May 2007, bre...@un... apparently wrote: 
> Here is a decimating filter module based on the 
> Savtsky-Golay method. 

License?
Is there a presumption that code posted to this
list is public domain?

Cheers,
Alan Isaac

James Battat wrote:
> Hello,
>
> (for a 2-d plot)
> Any example code of how to label the 2nd y-axis using a different scale
> than the first y-axis for the same dataset?
>
> For example, how do you make a plot of distances with the left y-axis in
> kilometers and the right y-axis in miles?
>
> Thanks in advance for your help,
> James
>   

James:  Use twinx - as demonstrated in thee 'two_scales.py' example.

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hello,

(for a 2-d plot)
Any example code of how to label the 2nd y-axis using a different scale
than the first y-axis for the same dataset?

For example, how do you make a plot of distances with the left y-axis in
kilometers and the right y-axis in miles?

Thanks in advance for your help,
James

Hello, I'm getting this error when using two consecutive plot_dates():

  File "C:\Python24\lib\site-packages\matplotlib\axes.py", line 1565, in xaxis_d ate
    formatter = AutoDateFormatter(locator)
UnboundLocalError: local variable 'locator' referenced before assignment

I've tested using just three lines of code:

>From pylab import *
plot_date([783746, 783747, 783748], [1,2,3])
plot_date([783749, 783750, 783751], [1,2,3])

thanks,

Jeff


       
---------------------------------
Moody friends. Drama queens. Your life? Nope! - their life, your story.
 Play Sims Stories at Yahoo! Games. 

Hi,

We are starting to require plotting large data sets.
600K samples is one second, and we have 20 sec runs

This takes approx 5 min to draw the plots on screen.
Then if you want to zoom, ... well go get a cup of coffee, ... not very 
productive.

1) Is MatPlotLib the right tool for large data sets, .. should I be 
looking at something else?

2) Given nothing else better, I'm looking for suggestions how to handle 
this size data.

My initial thoughts, ... display a low res graph, then have some movable 
markers in the low res graph and the main graph would only show the 
contents between those markers.
( ala some sound editing programs )

This would mean I need to filter/decimate the data for the low res 
graph, .. and a quick search on the web didn't seem to turn up any 
python way of doing this, .. anyone know of any existing python tool set 
to do this, before I re-invent the wheel?

Thanks for any input
Steve

Emmanuel Favre-Nicolin wrote:
> Hi,
>
> I can plot only one time in windows. The second time, the window 
> appears without the tools and when I click on the windows it become 
> white and freezes. Here is a code :
>
> from pylab import *
> x=arange(5)
> y=x*x
> plot(x,y)
> show()
> plot(x,y)
> show()
Emmanuel:

Quoting from the the FAQ (http://matplotlib.sourceforge.net/faq.html):

" It is possible to force matplotlib to draw after every command, which 
is what you want in interactive mode 
<http://matplotlib.sourceforge.net/interactive.html>, but in a script 
you want to defer all drawing until the script has executed. This is 
especially important for complex figures that take some time to draw. 
'show' is designed to tell matplotlib that you're all done issuing 
commands and you want to draw the figure now. In the TkAgg backend, 
which can be used from an arbitrary python shell interactively, it also 
sets interactive mode. So you can launch your script with python -i 
myscript.py -dTkAgg and then change it interactively from the shell. 
IMPORTANT: show should called at most once per script and it should be 
the last line of your script. At that point, the GUI takes control of 
the interpreter. If you want to force a figure draw, use draw 
<http://matplotlib.sourceforge.net/matplotlib.pylab.html#-draw> instead."

-Jeff



      -- 

Jeffrey S. Whitaker         Phone : (303)497-6313
NOAA/OAR/CDC  R/PSD1        FAX   : (303)497-6449
325 Broadway                Boulder, CO, USA 80305-3328

Hi,

I can plot only one time in windows. The second time, the window appears
without the tools and when I click on the windows it become white and
freezes. Here is a code :

from pylab import *
x=arange(5)
y=x*x
plot(x,y)
show()
plot(x,y)
show()

James Boyle wrote:
> Thanks Jeff,  it works.
> where is the reference to explain exactly what 'zorder' does and its 
> proper use?
>
> --Jim
>

Jim:  See zorder_demo.py in the examples - the comments explain it 
pretty well. I've cut and pasted below:

"""
The default drawing order for axes is patches, lines, text.  This
order is determined by the zorder attribute.  The following defaults
are set

Artist                      Z-order
Patch / PatchCollection      1
Line2D / LineCollection      2
Text                         3

You can change the order for individual artists by setting the zorder.  Any
individual plot() call can set a value for the zorder of that particular 
item.

In the fist subplot below, the lines are drawn above the patch
collection from the scatter, which is the default.

In the subplot below, the order is reversed.

The second figure shows how to control the zorder of individual lines.
"""


-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-124
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi,

=20

I'm making contour plots of a field distribution, and overlaid on that
is a grid that I create using hlines() and vlines().  I want to change
the contour plot many times, but keep the grid the same.  Right now, I
have clear the axes with cla() then plot the new contour and replot the
grid.  This slows things down a lot, and I'm wondering if anyone knows
of a way to update the contour plot without replotting the grid.

=20

thanks,

trevis

=20

________________________________________________

=20

Trevis Crane

Postdoctoral Research Assoc.

Department of Physics

University of Ilinois

1110 W. Green St.

Urbana, IL 61801

=20

p: 217-244-8652

f: 217-244-2278

e: tc...@ui...

________________________________________________

=20

Hi all,
I think there may be a bug in annotate. If I don't have any offset
between the xcoord of xy and xytext I get a zero division error.
Otherwise it is fine. For example:

In [3]: plot([1,2,3],[1,2,3])
Out[3]: [<matplotlib.lines.Line2D instance at 0x8cec96c>]

In [4]: annotate('hello', xy=(2.0,2.0), xytext=(2.0,1.5),
arrowprops=dict(facecolor='black'))
---------------------------------------------------------------------------
<type 'exceptions.ZeroDivisionError'>     Traceback (most recent call last)

<SNIP>

/usr/lib/python2.5/site-packages/matplotlib/patches.py in
getpoints(self, x1, y1, x2, y2, k)
    665         """
    666         x1,y1,x2,y2,k = map(float, (x1,y1,x2,y2,k))
--> 667         m = (y2-y1)/(x2-x1)
    668         pm = -1./m
    669         a = 1

<type 'exceptions.ZeroDivisionError'>: float division

It looks quite clear where the problem is. Though I'm not sure I'm up
to making a patch.

Cheers,
John